Queue projects for MCMC analysis

EnqueueMC() automates the complete setup of MCMC analyses across multiple projects and model definitions. It constructs matrices, prepares RevBayes repositories and scripts, and generates SLURM job files where needed.

EnqueueMC(projects, models, overwrite = TRUE)

Arguments

projects

Character vector of project identifiers.

models

Character vector of RevBayes model identifiers.

overwrite

Logical. Whether to overwrite existing processed matrices. Defaults to TRUE.

Value

EnqueueMC() invisibly returns NULL. The function is called for its side-effect of generating and enqueuing RevBayes MCMC analyses on the configured cluster.

Details

For each project in projects, EnqueueMC():

1. Calls PrepareMatrix() to ensure up-to-date NEXUS matrices.

2. Uses RevBayes() to copy or generate RevBayes scripts.

3. Checks for an existing convergence file via ConvergenceFile().

4. If missing or incomplete, creates MCMC SLURM job files with MakeSlurm(ml = FALSE).

The function uses cli::cli_progress_message() to display progress and finishes with cli::cli_progress_done().

See also

EnqueueML() for marginal likelihood estimation, RevBayes(), MakeSlurm(), PrepareMatrix()